Contacts of the helix formed by residues 168 - 175 (chain A) in PDB entry 4Q44
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PHE* 5.4 3.5 - - - -
163A VAL 3.2 23.3 - - - +
164A ILE* 3.7 5.9 - - + +
165A THR* 2.8 37.4 + - - +
167A ALA* 1.3 80.1 - - + +
169A VAL* 1.3 64.5 + - - +
170A PRO* 3.5 0.7 - - - -
171A ALA* 3.5 8.9 + - - +
172A PHE* 3.0 24.5 + - + +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PRO* 4.3 9.6 - - + -
148A LEU* 3.9 20.6 - - + -
164A ILE* 3.8 14.6 - - + -
165A THR 3.0 19.0 + - - +
166A PRO* 3.7 14.8 - - + +
168A GLU* 1.3 77.2 - - - +
170A PRO* 1.3 65.9 - - + +
172A PHE* 3.1 7.0 + - - +
173A LEU* 2.8 51.0 + - + +
227A GLN 5.2 1.3 - - - +
228A GLY* 4.6 8.5 - - - +
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Residues in contact with PRO 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PRO 3.6 11.0 - - - +
167A ALA 3.8 9.2 - - - +
168A GLU 3.6 2.5 - - - -
169A VAL* 1.3 96.6 - - + +
171A ALA* 1.3 61.3 - - - +
173A LEU* 3.3 17.0 + - + +
174A GLN* 3.3 18.6 + - - +
204A GLN* 5.2 2.1 + - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ALA 5.3 0.2 + - - -
168A GLU* 3.5 10.0 + - - +
169A VAL 3.3 0.4 - - - -
170A PRO* 1.3 80.5 - - - +
172A PHE* 1.3 62.5 + - - +
174A GLN* 3.7 16.0 + - - +
175A THR* 4.3 7.6 + - - +
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.7 24.2 - - + -
151A ILE* 3.9 11.4 - - + -
155A MET* 3.7 35.4 - - + -
162A PHE* 4.3 6.3 - + - -
164A ILE* 3.6 33.2 - - + -
168A GLU* 3.0 20.9 + - + +
169A VAL* 3.4 7.6 - - - +
171A ALA* 1.3 79.1 - - - +
173A LEU* 1.3 62.6 + - + +
174A GLN 3.6 0.2 + - - -
175A THR* 4.1 4.0 + - - -
176A LEU* 3.3 41.0 + - + +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 4.3 10.5 - - + -
148A LEU* 4.6 7.9 - - + -
169A VAL* 2.8 31.8 + - + +
170A PRO* 3.3 8.2 + - + +
172A PHE* 1.3 77.2 - - + +
174A GLN* 1.3 65.2 + - - +
176A LEU* 3.1 29.7 + - + +
200A CYS* 3.1 26.0 - - + +
201A GLY 4.5 0.4 - - - -
204A GLN* 3.8 14.4 - - - +
225A ARG 3.8 16.6 - - - +
226A SER 3.4 18.6 - - - +
227A GLN 3.6 6.7 - - - +
228A GLY* 3.5 21.5 - - - +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PRO 3.3 11.5 + - - +
171A ALA* 3.9 12.1 - - - +
172A PHE 3.4 0.8 - - - -
173A LEU* 1.3 80.8 - - - +
175A THR* 1.3 65.6 + - + +
199A THR* 3.3 23.4 + - - +
201A GLY* 3.4 21.4 + - - +
204A GLN* 3.1 24.7 + - - +
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA 4.3 7.8 + - - -
172A PHE* 4.1 4.5 + - - -
173A LEU 3.4 0.2 - - - -
174A GLN* 1.3 81.4 - - + +
176A LEU* 1.3 57.2 + - - +
177A PRO* 3.2 12.7 - - - +
198A ARG* 5.3 4.8 + - - +
199A THR* 4.3 10.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il